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Department of Plant Pathology

Department of Plant Pathology
Kansas State University
1712 Claflin Road
4024 Throckmorton PSC
Manhattan, KS 66506

Ph: +1-785-532-6176
Fx: +1-785-532-5692

2019 Projects


Projects below are sorted by last name of mentors.



Gene editing to develop improved wheat varieties

CRISPR/CAS9 technology can be used to rapidly generate new variants of genes with improved function. We use CAS9 technology to edit wheat genes that can increase yield and disease resistance, and improve nutritional quality. Intern will be involved in selecting genes that affect positively these traits in wheat, designing CRISPR/CAS9 reagents for gene editing using bioinformatical tools, and testing these reagents using next-generation sequencing (NGS) technologies available at the KSU Integrated Genomics Facility. She/he will conduct these experiments as part of the gene editing projects aimed at improving wheat traits. 

60% lab, 40% computer.

MentorEduard Akhunov 


Building puzzles with fungal DNA

Have you heard of DNA sequencing but you're not quite sure what it is? Maybe you've had a class or heard a news article that discussed an assembled genome but it is not clear what is assembled or what it even looks like. Complete an internship in the Cook lab as part of the K-State REEU program and get hands on experience extracting fungal DNA, preparing sequencing libraries for both short and long-read sequencing and learn basic bioinformatic skills. You will leave with proficiency and knowledge about DNA sequencing and the types of experimental questions that can be addressed.

Areas: Genomics, mycology, molecular biology, bioinformatics, and plant pathology.

MentorDavid Cook


Characterizing virus resistance in wheat breeding populations and sequencing of field virus collections

The student will aid in genetic population screening, virus detection assays, learn DNA isolation and DNA sequencing. Lab: 60%, Greenhouse: 30%, Field: 10%.

MentorJohn Fellers

tania kim


Crop diversity effects on pest and beneficial insects

Crop plants are vulnerable to pest infestation. As such, the US spends $12.5 billion/year for pesticides, however, more sustainable measures are needed to control pest outbreak.  For example, planting different crop types or varieties can reduce the likelihood of damage to target crop plants. For this project, we will examine how crop diversity (monocultures versus polycultures, annual versus perennial crop species) affects the likelihood of infestation and damage by pests such as aphids.  We will also examine how crop diversity affects the likelihood of colonization of important predatory insects (e.g. lady beetles) that naturally feed on aphids and pollinators.

Field 50%/Greenhouse 25%/Lab 25%.

Mentor:  Tania Kim




dal hoe

Wild wheat!

Just like we all have some interesting relatives, wheat has some wild in-laws of its own! Bread wheat was domesticated in Central Asia around Iran and Iraq and the wild relatives can still be found there today. Though they don’t really even look like wheat and aren’t any good for making bread, the wild relatives have important genes for disease resistance. Using chromosome engineering and bioinformatics, we are transferring these useful genes into wheat to make stronger wheat plants that are resistant to disease and other stress.

Areas: genetics and genomics, plant breeding, plant pathology, cytogenetics.

MentorsDal-Hoe Koo and Jesse Poland



s liu

What makes plants resistant to diseases?

Plants do not have immune systems like ours, but they fight off pathogens. Some plants have a strong capability to fight against diseases but some do not. In this project you will inoculate plant pathogenic bacteria on plants (e.g. wheat and corn), observe symptom developing through time-lapse imaging, and quantify disease resistant levels among plant individuals.  You will also use DNA technologies to find genomic regions causing resistance.You will learn basic programming, cutting-edge computation techniques for data processing and visualization, and knowledge in plant diseases, genetics, and genomics.

Lab 60%/Greenhouse 30%/Field 10%.

MentorSanzhen Liu



brian mccornack

Blending ecology with technology to manage crop pests

Kansas crop growers face a diverse array of insect pests and need to adapt novel solutions to manage arthropods. In this project, you will learn how to use cutting edge technology to help develop integrated pest management (IPM) solutions to pest problems and learn how to deliver information to growers using novel technologies. You will learn how to scout and sample insects, map prevalence across production fields, use sampling tools, and/or contribute to existing extension programs. In this program you will learn how social networks are digitally connecting farmers with researchers and Extension personnel to provide established user-networks for improved response to pest incursions.

Lab 25%/Field 50%/Computer 25%.

MentorBrian McCornack



New insect-associated viruses: Friends or Foes?  

Many plant pathogens rely on insect vectors for their transmission. Insects are occupied by native resident microorganisms from diverse groups ranging from bacteria to fungi to viruses, together called microbiome. Many of these microbes are not pathogen but they are beneficial. We recently discovered new insect-specific viruses associated with the Asian citrus psyllid, the natural vector of the causal agent of citrus greening disease in U.S. and other parts of the world. We consider the new viruses as natural components of the insect host`s microbiome. Join host-virus-vector interactions research team to explore the molecular interaction between the insect and its new viruses.

Areas: Virology, molecular biology, vector biology, and bioinformatics.

MentorShahideh Nouri


Establishing a high-throughput transformation platform for crop genome-phenome cause-effect studies

Functional genome analysis through genetic transformation and plant regeneration processes must enter the high-throughput stage in order to determine how these genome sequences generate crop phenotypes. However, functional genomics researches in most crops are constrained by low transformation efficiency. Establishment of a robust, reliable crop transformation and regeneration system for the use of ectopic overexpression, RNAi, and CRISPR/Cas9 gene editing approaches is crucial for understanding of the relationship between genomes and phenomes in the crops. You will learn crop (e.g., rice, maize, sorghum, tomato, lettuce, etc.) tissue culture, gene transformation, and genome editing technology.

MentorSanghun Park


y park

Insect hormone disruptors

Park team focuses on the development of new tools to disrupt insect endocrine system based on the knowledge of hormone receptors revealed in comparative genomics. Current project includes high throughput screening of chemical compounds that act on insect specific ecdysis triggering hormone receptor and mite specific neuropeptide receptors. Students will be trained for molecular biology and data analyses of bioassay depending on the background and the interests of the students assigned. Most of all, the students will have opportunities to play with arthropods, learn the fun biology, and perform modern molecular techniques to solve the problems in pest control.

MentorYoonseong Park



jesse poland

An eye in the sky...

Unmanned aerial vehicles (UAVs), sometimes called ‘drones’, are more than just fun toys to make cool videos. They are also powerful research tools that can help us quickly measure field experiments and farmer’s fields to measure plant growth and plant diseases. Join our research team to use UAVs for rapid measurements of plant traits and explore how this high-resolution data can be used for different analysis to understand plants.

Areas: physiology, engineering, genetics and genomics, high-throughput phenotyping.

MentorJesse Poland


 deann presley

Going undercover

Cover crops are used to prevent erosion and improve soil structure and have the added benefit of increasing the plant biodiversity of a cropping system. Does increasing biodiversity aboveground lead to increased biodiversity belowground, and if so, how does it affect the plant pathogenic organisms? In this project, you will collect measurements in the field and soil sample experiments with and without cover crops to determine if there are any effects of cover crops on soil health.

50%, Field, 50% Lab.

MentorDeAnn Presley



davina rhodes

Carotenoid Biofortification of Sorghum

We are developing genomic tools to increase pro-Vitamin A carotenoids in sorghum grain, a dietary staple grown by millions of people in marginal environments in sub-Saharan Africa, Asia, and the Americas, where vitamin A deficiencies are prevalent. As part of our project, the student could be involved in measuring agronomic traits in the field, extracting and measuring sorghum grain carotenoids, and isolating RNA for carotenoid gene expression analysis. The student could also learn to manipulate large data sets and gain experience programming in R.

Lab 50%, Field 25%, Computer 25%

MentorDavina Rhodes



My feet hurt! Investigating root rots in diversified cropping systems of wheat

Once upon a time, farmers used to grow wheat, followed by a year of giving the field a rest, called a fallow period. Fallow was meant to recharge the soil with moisture and fertility that could be used in the following cropping cycle. However, with the population growing and farming becoming an economic challenge, wheat growers are looking for new rotations that can make a profit. Peas are now being grown in place of fallow in many regions, including northern KS. While they do use the moisture saved for the wheat crop, their Rhizobia fix nitrogen to improve fertility. But, it may come with a cost. During this project, you will investigate if root rot pathogens that affect both wheat and pea are building up in the soil due to these cropping systems. This will include trips to sample wheat and pea across northern KS and culturing these pathogens in the lab. The pathogen communities will then be compared to wheat-fallow systems. Could we be driving a system we can't control?

Field 50%, Lab 50%

MentorJessica Rupp


Extracellular vesicles as intercellular messengers

Extracelluar vesicles are important intercellular messengers in many organisms, but very little is known about them in insects or how they might be used for insect control and plant protection. My lab is working to address these shortcomings by enhancing our understanding of the composition of these vesicles and the roles they play in intercellular communication in insects. Experiments will focus on identifying protein and RNA content of insect-derived extracellular vesicles and examining their uptake by cultured insect cells in an effort to devise ways that they may be used in pest control. Interns will learn multiple molecular techniques including gene expression analysis and double-stranded RNA design, synthesis, and delivery. In addition, interns will also have the opportunity to learn cell culture and fluorescent microscopy techniques.

MentorKristopher Silver

bin tian


Super plants

Advanced modern biotechnology has changed many aspects in agriculture. Recent rapidly developed genome editing technology such as CRISPR/Cas9 is changing the world in agriculture as well as human medicine. In this project, you will learn how to design, construct, and use engineered plasmid vectors to introduce new traits by expressing genes and/or genome editing in plants (wheat or soybean). You will gain knowledge about the interaction between viral pathogens and plant hosts. You will also use confocal microscopy to observe fluorescent gene markers. You will gain skills in molecular biology, plant transformation and micropropagation, as well as DNA/RNA extraction, and virus biology, virus detection and analysis.

Lab: 80%, Greenhouse 20%.

MentorBin Tian




Fungal genomics to understand Fusarium pathogen diversity

Fusarium is a genus of filamentous fungi that contains many plant pathogens that cause diseases on major crops. In this project, you will use DNA sequence from fungal samples to analyze genetic diversity, infer the evolutionary history of populations, and associate genetic markers with important pathogen traits. This project will expand your knowledge of: microbiological techniques such as culturing fungal isolates and measuring growth rates; molecular techniques such as nucleic acid extraction and amplification, and DNA sequencing; and bioinformatics techniques such as next-generation DNA sequence processing and analysis of genetic diversity.

Lab: 50% Computer: 50%

MentorChristopher Toomajian



Biotechnology for crop improvement

From host an internship for the REEU on the following topic: biotechnology is an awesome and powerful tool to improve plants. You will have several options to improve plant health (especially wheat and soybean) in terms of pathogen protection and tolerance to extreme environmental factors. You will learn how different make DNA vector constructions, how to introduce these vectors into plants using the gene gun or Agrobacterium-mediated transformation, what it take to identify and regenerate these plants containing new traits, and how these traits are put into use in the field. Techniques learned in these projects can be applicable to many other areas of interest.

70% lab 15% computer 15% field.

MentorHarold Trick


Help Control a Cereal Killer

A fungus, called Magnaporthe oryzae, causes blast disease that destroys enough rice every year to feed 60 million people.  This fungus adapted to infect wheat in the 1980s, and now threatens global wheat production as well.  Have a blast understanding how the fungus kills cereal crops at the molecular and cellular level.  You will learn live cell imaging using confocal and fluorescence microscopy to observe the fungus invading rice cells.  Learn to document locations and dynamics of fluorescently labeled fungal effector proteins, critical tools the fungus uses to hijack host cells and cause disease.  You will also gain skills in molecular biology, construction of fluorescent fungal strains, and rice infection assays. 

Lab 100% 

MentorBarbara Valent


Mechanisms affecting RNAi efficiency in insects

RNA interference (RNAi) is a Nobel Prize-winning discovery of the post-transcriptional gene regulatory mechanism and has shown great potentials for developing novel strategies for managing insect pests. However, RNAi efficiency is considerably variable among different insect species, which have currently hindered possible applications of RNAi-based strategies for managing insect pests in different taxonomic groups. Our lab is studying molecular mechanisms affecting RNAi efficiency in different insect species. In this research, you will learn various molecular techniques, including identification and analysis of insect genes, design and synthesis of double-stranded RNA (dsRNA), dsRNA delivery, and gene expression analysis.

Lab 100%

MentorKun Yan Zhu